Blueprints can be a folder or zip. The Blueprint folder would contain a WordPress Installation and any plugins or themes you would like. You can also edit the wp-config.php file and add defines and change the database table prefix.

With the Premium version you can create a site, set the permlanks add users, add plugins and activate, etc. Then export the website into the blueprints folder and it will that as the template.

Yes after you create a Blueprint you would normally want to stop and restart the web and database services(first selection on the main menu) for DesktopServer to add your blueprint to the list